User: Johannes Rainer

gravatar for Johannes Rainer
Reputation:
980
Status:
Trusted
Location:
Italy
Twitter:
@jotsetung
Last seen:
an hour ago
Joined:
2 years, 11 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 202 results • page 1 of 21 • next >
0
votes
1
answers
23
views
1
answers
Comment: C: XCMS obiwarp adjustRtime issue
... Good news is from the version you are using (1.52.0) to the current version (2.99.10) there have been many changes, improvements and fixes. Unfortunately we couldn't merge all fixes into the Bioconductor 3.5 release version because of some nasty git/svn complications. Now, Bioconductor release 3.6 ...
written 1 hour ago by Johannes Rainer980
0
votes
1
answers
23
views
1
answers
Answer: A: XCMS obiwarp adjustRtime issue
... Hi, this has to do most likely with the binning of the data. Try using a different binSize for the ObiwarpParam, e.g. binSize = 2. And what version of xcms are you using? Could you please provide the full output of the sessionInfo? Would it be possible for you to share the data so I could have a c ...
written 3 hours ago by Johannes Rainer980
0
votes
2
answers
96
views
2
answers
Comment: C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... I would use the first one - or the second, which to my understanding contains only genes encoded on chromosomes (the other might contain also containing genes encoded in contigs). ...
written 27 days ago by Johannes Rainer980
0
votes
2
answers
96
views
2
answers
Answer: A: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... Ensemblgenomes provides gene models for many plants. Check http://plants.ensembl.org/index.html . You could either download a gtf or gff3 file for rice from there and build a TxDb using makeTxDbFromGff (GenomicFeatures package) or, since the data is in Ensembl format, an EnsDb using ensDbFromGtf (en ...
written 28 days ago by Johannes Rainer980
0
votes
1
answers
161
views
1
answers
Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... Sorry, I was unclear. I didn't mean to remove the AnnotatioHub folder from the R library. AnnotationHub creates a hidden folder (called ".AnnotationHub" (note the dot before AnnotationHub), usually in the user's home directory. The cache as well as the database is stored there. You should re-instal ...
written 5 weeks ago by Johannes Rainer980
0
votes
1
answers
161
views
1
answers
Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... That you don't get any results for the query in AnnotationHub is strange. Could you try to delete the .AnnotationHub folder in your home directory and re-run the commands above? Eventually the AnnotationHub database is still the one from your previous installation. ...
written 5 weeks ago by Johannes Rainer980
0
votes
1
answers
161
views
1
answers
Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... Checked into the problematic transcript: transcript ENST00000639671 was assigned to gene ENSG00000141198 in Ensembl release 88, but got re-assigned in Ensembl 90 to ENSG00000166260. Both genes are encoded at around the same region on chromosome 17, but on opposite strands. The order of the exons of ...
written 5 weeks ago by Johannes Rainer980
0
votes
1
answers
161
views
1
answers
Answer: A: ensDbFromGtf error from gtf file downloaded from GENCODE.
... Regarding the GENCODE gtf file - for that you might want to use the makeTxDbFromGFF function from the GenomicFeatures package since the ensembldb::ensDbFromGtf works only for gtf files from Ensembl as it requires certain fields/columns to be present in the file. Regarding the error you get with the ...
written 5 weeks ago by Johannes Rainer980
0
votes
3
answers
263
views
3
answers
Answer: A: org.Hs.eg.db error same ensembl ID in different genes
... If you're working with Ensembl annotations I would stick to annotation resources that were built on Ensembl provided data (such as biomaRt or ensembldb). This also avoids potential problems and multi-mappings between Ensembl and NCBI. AFAIK the .eg. packages are built using information from NCBI and ...
written 6 weeks ago by Johannes Rainer980
1
vote
0
answers
253
views
0
answers
News: ensembl 90 ensembldb EnsDb databases have been added to AnnotationHub
... Hi all! ensembldb EnsDb databases for 78 species from Ensembl version 90 are now available through AnnotationHub (devel branch). cheers, jo > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2017-08-31 > query(ah, c("EnsDb", "v90")) AnnotationHub with 78 records # snaps ...
annotation annotationhub news ensembl ensemblb written 7 weeks ago by Johannes Rainer980

Latest awards to Johannes Rainer

Scholar 4 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 4 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 5 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 6 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 6 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 18 months ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
Scholar 18 months ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 18 months ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 18 months ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 18 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Popular Question 21 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Appreciated 22 months ago, created a post with more than 5 votes. For A: biomaRt no longer works with proxy after upgrade
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Centurion 23 months ago, created 100 posts.
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 23 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 23 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Supporter 23 months ago, voted at least 25 times.
Scholar 23 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Autobiographer 2.4 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 301 users visited in the last hour